New windows/doors after insulation wrap

Depends on what you define as a huge problem. :)

If your OK with the internal reveals being knocked out and then reinstated, then you could retrofit that way. If the original windows were left in position at the inner-side of the outer leaf and not pushed further outwards to the threshold of the new insulation, then the new windows should be pushed outwards so that they follow best practice and close off the cold loop at the reveal.

So yes, it's a big job but one which is important to get right. That might require that you have both an experienced builder as well as a patient window installer so that the air-tightness is completed in full, as most or all window installers refuse to engage in applying air-tightness tape and see it a the builders job to do so.

It's common because it's less hassle and cheaper. It's an easier sell too if you're not into having plasterers redoing the reveals, so I can understand how it happens, but it's just not in the true spirit of doing the job properly!

To get it retrofitted properly? Yes.

Window installers are likely to offer to carry out the job by mounting the window frames into the existing orifice as opposed to mounting them into the EWI as they should be. That usually means using expanding foam between the window frame and the reveal and often doesn't close the insulation to the same quality as it would had the windows been pushed outwards during wrapping. It also likely exposes more window-frame to the exterior than if the window has been fitted properly, a concern as the frame area has a higher heat-loss than than triple-glazing, so you're then getting a thermally less-effective windows as well as less effective reveals.

Then the cill has to be retrofitted and sealed to match the new window, the risk there is with damaging the existing finish or ending up with a less effective solution.

That why when you're wrapping you really need to be looking critically at the extincting windows and if they're under spec, costing the replacement of them into the overall project scope.

Here's a UK link and image showing how it should be done:

https://retrofit.support/detail/73/

Ah, bay windows may sometimes be the exception due to structural elements within the frames or cost, or maybe even complexity around the internal reveal or detailing concerns brought up by the client. Who knows. It's a compromise in many ways, the EWI may have been financially unattainable if new windows were factored in.

Have you any idea how to find a company to do this properly?

I know. It took me 4 years (2010 to 2014) to find the right builder to take it on. Shocking the number of so called insulation expert companies I had over the floor who hadn't a clue what thermal bridging is. Only really interested in doing a quick job, getting the grant and moving onto the next job.